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- EMDB-16960: Murine type III Abeta fibril from ARTE10 mouse -

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Basic information

Entry
Database: EMDB / ID: EMD-16960
TitleMurine type III Abeta fibril from ARTE10 mouse
Map dataEx vivo Abeta40 fibril from ARTE10 mouse brain.
Sample
  • Complex: Amyloid fibril of amyloid-beta
    • Protein or peptide: Amyloid-beta protein 42
KeywordsAmyloid fibril / PROTEIN FIBRIL
Function / homology
Function and homology information


negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / axo-dendritic transport / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / synaptic assembly at neuromuscular junction / axon midline choice point recognition ...negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / axo-dendritic transport / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / synaptic assembly at neuromuscular junction / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / mating behavior / regulation of spontaneous synaptic transmission / signaling receptor activator activity / ciliary rootlet / Golgi-associated vesicle / Lysosome Vesicle Biogenesis / PTB domain binding / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / COPII-coated ER to Golgi transport vesicle / suckling behavior / dendrite development / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / presynaptic active zone / neuromuscular process controlling balance / The NLRP3 inflammasome / Advanced glycosylation endproduct receptor signaling / negative regulation of long-term synaptic potentiation / regulation of presynapse assembly / regulation of multicellular organism growth / transition metal ion binding / intracellular copper ion homeostasis / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / regulation of peptidyl-tyrosine phosphorylation / smooth endoplasmic reticulum / Purinergic signaling in leishmaniasis infection / protein serine/threonine kinase binding / positive regulation of chemokine production / forebrain development / clathrin-coated pit / Notch signaling pathway / neuron projection maintenance / positive regulation of G2/M transition of mitotic cell cycle / Mitochondrial protein degradation / positive regulation of protein metabolic process / extracellular matrix organization / ionotropic glutamate receptor signaling pathway / positive regulation of mitotic cell cycle / response to interleukin-1 / positive regulation of peptidyl-threonine phosphorylation / cholesterol metabolic process / positive regulation of calcium-mediated signaling / axonogenesis / negative regulation of peptidase activity / positive regulation of glycolytic process / adult locomotory behavior / trans-Golgi network membrane / platelet alpha granule lumen / dendritic shaft / central nervous system development / positive regulation of interleukin-1 beta production / learning / positive regulation of long-term synaptic potentiation / endosome lumen / astrocyte activation / locomotory behavior / Post-translational protein phosphorylation / positive regulation of JNK cascade / microglial cell activation / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / synapse organization / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of non-canonical NF-kappaB signal transduction / visual learning / neuromuscular junction / recycling endosome / positive regulation of peptidyl-serine phosphorylation / cognition / Golgi lumen / positive regulation of interleukin-6 production / neuron cellular homeostasis / positive regulation of inflammatory response / endocytosis / neuron projection development / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / G2/M transition of mitotic cell cycle / positive regulation of tumor necrosis factor production / cell-cell junction
Similarity search - Function
Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site ...Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZielinski M / Peralta Reyes FS / Gremer L / Schemmert S / Frieg B / Willuweit A / Donner L / Elvers M / Nilsson LNG / Syvanen S ...Zielinski M / Peralta Reyes FS / Gremer L / Schemmert S / Frieg B / Willuweit A / Donner L / Elvers M / Nilsson LNG / Syvanen S / Sehlin D / Ingelsson M / Willbold D / Schroeder GF
Funding support Germany, Sweden, 5 items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research16LW028 Germany
Swedish Research Council2021-02793 Sweden
Swedish Research Council2021-01083 Sweden
Swedish Research Council2021-03524 Sweden
Helmholtz Association Germany
CitationJournal: Nat Neurosci / Year: 2023
Title: Cryo-EM of Aβ fibrils from mouse models find tg-APP fibrils resemble those found in patients with sporadic Alzheimer's disease.
Authors: Mara Zielinski / Fernanda S Peralta Reyes / Lothar Gremer / Sarah Schemmert / Benedikt Frieg / Luisa U Schäfer / Antje Willuweit / Lili Donner / Margitta Elvers / Lars N G Nilsson / Stina ...Authors: Mara Zielinski / Fernanda S Peralta Reyes / Lothar Gremer / Sarah Schemmert / Benedikt Frieg / Luisa U Schäfer / Antje Willuweit / Lili Donner / Margitta Elvers / Lars N G Nilsson / Stina Syvänen / Dag Sehlin / Martin Ingelsson / Dieter Willbold / Gunnar F Schröder /
Abstract: The use of transgenic mice displaying amyloid-β (Aβ) brain pathology has been essential for the preclinical assessment of new treatment strategies for Alzheimer's disease. However, the properties ...The use of transgenic mice displaying amyloid-β (Aβ) brain pathology has been essential for the preclinical assessment of new treatment strategies for Alzheimer's disease. However, the properties of Aβ in such mice have not been systematically compared to Aβ in the brains of patients with Alzheimer's disease. Here, we determined the structures of nine ex vivo Aβ fibrils from six different mouse models by cryogenic-electron microscopy. We found novel Aβ fibril structures in the APP/PS1, ARTE10 and tg-SwDI models, whereas the human type II filament fold was found in the ARTE10, tg-APP and APP23 models. The tg-APP mice showed an Aβ fibril whose structure resembles the human type I filament found in patients with sporadic Alzheimer's disease. A detailed assessment of the Aβ fibril structure is key to the selection of adequate mouse models for the preclinical development of novel plaque-targeting therapeutics and positron emission tomography imaging tracers in Alzheimer's disease.
History
DepositionMar 30, 2023-
Header (metadata) releaseNov 29, 2023-
Map releaseNov 29, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16960.png

Downloads & links

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Map

FileDownload / File: emd_16960.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEx vivo Abeta40 fibril from ARTE10 mouse brain.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 300 pix.
= 242.4 Å		0.81 Å/pix.
x 300 pix.
= 242.4 Å		0.81 Å/pix.
x 300 pix.
= 242.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.808 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.17
Minimum - Maximum-15.164942 - 21.391494999999999
Average (Standard dev.)-0.000000000005382 (±1.0011961)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 242.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Ex vivo Abeta40 fibril from ARTE10 mouse brain. Half map 1.

Fileemd_16960_half_map_1.map
AnnotationEx vivo Abeta40 fibril from ARTE10 mouse brain. Half map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Ex vivo Abeta40 fibril from ARTE10 mouse brain. Half map 2.

Fileemd_16960_half_map_2.map
AnnotationEx vivo Abeta40 fibril from ARTE10 mouse brain. Half map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Amyloid fibril of amyloid-beta

EntireName: Amyloid fibril of amyloid-beta
Components
  • Complex: Amyloid fibril of amyloid-beta
    • Protein or peptide: Amyloid-beta protein 42

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Supramolecule #1: Amyloid fibril of amyloid-beta

SupramoleculeName: Amyloid fibril of amyloid-beta / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20 kDa/nm

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Macromolecule #1: Amyloid-beta protein 42

MacromoleculeName: Amyloid-beta protein 42 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.520087 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV IA

UniProtKB: Amyloid-beta precursor protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 9521 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.74 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.91 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10369
Startup modelType of model: OTHER / Details: Cylinder.
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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